[Analogue-commits] r127 - pkg/man

[noreply at r-forge.r-project.org]

Author: gsimpson
Date: 2009-05-30 00:19:39 +0200 (Sat, 30 May 2009)
New Revision: 127

Modified:
   pkg/man/wa.Rd
Log:
Clarified what happens to small tolerances by default

Modified: pkg/man/wa.Rd
===================================================================
--- pkg/man/wa.Rd	2009-05-27 22:33:50 UTC (rev 126)
+++ pkg/man/wa.Rd	2009-05-29 22:19:39 UTC (rev 127)
@@ -48,7 +48,7 @@
     missing.}
   \item{small.tol}{character; method to replace small tolerances. See Details.}
   \item{min.tol}{numeric; threshold below which tolerances are treated
-    as being \sQuote{small}.}
+    as being \sQuote{small}. Default is not to replace small tolerances.}
   \item{f}{numeric, \eqn{0 < f < 1}; fraction of environmental gradient
     \code{env} to replace small tolerances with if \code{small.tol =
       "fraction"} is specified.}
@@ -85,9 +85,13 @@
   Species that have very small tolerances can dominate reconstructed
   values if tolerance down-weighting is used. In \code{wa}, small
   tolerances are defined as a tolerance that is \eqn{<}
-  \code{min.tol}. These small tolerances can be adjusted in several
-  ways:
+  \code{min.tol}. The default is to not replace small tolerances, and
+  the user needs to specify suitable values of \code{min.tol}. Function
+  \code{\link{tolerance}} may be of use in computing tolerances before
+  fitting the WA model.
 
+  Small tolerances can be adjusted in several ways:
+
   \describe{
     \item{\code{min} }{small tolerances are replaced by the smallest
       observed tolerance that is greater than, or equal to,